Special

MmuINT0128564 @ mm9

Intron Retention

Gene
ENSMUSG00000032487 | Ptgs2
Description
prostaglandin-endoperoxide synthase 2 [Source:MGI Symbol;Acc:MGI:97798]
Coordinates
chr1:151952072-151955142:+
Coord C1 exon
chr1:151952072-151952219
Coord A exon
chr1:151952220-151952502
Coord C2 exon
chr1:151952503-151955142
Length
283 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGG
5' ss Score
10.07
3' ss Seq
CTATCTTTGGTACCTTCCAGGAG
3' ss Score
8.51
Exon sequences
Seq C1 exon
GTTGCTGGGGGAAGAAATGTGCCAATTGCTGTACAAGCAGTGGCAAAGGCCTCCATTGACCAGAGCAGAGAGATGAAATACCAGTCTCTCAATGAGTACCGCAAACGCTTCTCCCTGAAGCCGTACACATCATTTGAAGAACTTACAG
Seq A exon
GTGAGGAATGGTTTCTAAATTTTCTAAAAGGATCAGGGATTAAGTGGGAAAAGAGAACGTGAGAGGGCATTTAGTGAAGGGATAAACTATCTTCCTCTTCCTCCTCCTCCTCCTCCTTTTCTTCTTCTTCTTCTAGAAATAGAAAAGGACCGAGTTTACTGAGAAAGAGGAGTGGGAATGGGGTCAGCTAGTGAGCGGGGGAAAGCCTATGCTCAACAGCCAGGACAATTGTCACCCGTTCCCAGTTTGATGTTCCTGTATCTCTATCTTTGGTACCTTCCAG
Seq C2 exon
GAGAGAAGGAAATGGCTGCAGAATTGAAAGCCCTCTACAGTGACATCGATGTCATGGAACTGTACCCTGCCCTGCTGGTGGAAAAACCTCGTCCAGATGCTATCTTTGGGGAGACCATGGTAGAGCTTGGAGCACCATTCTCCTTGAAAGGACTTATGGGAAATCCCATCTGTTCTCCTCAATACTGGAAGCCGAGCACCTTTGGAGGCGAAGTGGGTTTTAAGATCATCAATACTGCCTCAATTCAGTCTCTCATCTGCAATAATGTGAAGGGGTGTCCCTTCACTTCTTTCAATGTGCAAGATCCACAGCCTACCAAAACAGCCACCATCAATGCAAGTGCCTCCCACTCCAGACTAGATGACATTAACCCTACAGTACTAATCAAAAGGCGTTCAACTGAGCTGTAAAAGTCTACTGACCATATTTATTTATTTATGTGAAGAATTTAATTTAATTATTTAATATTTATACTGAATTTTTTTTCATGTAACATCTTCCATAACAGAAGGCAATGTTCTTGAACAATGTTACATTTGTGAAGATTCCCTCCGGTGTTTGTCCTTTAAATATGTGTTACCTGAAACTGAAAGGAAATCAGCATTCATTCCTCTACATAAGCCAGTGAGAAGGGAAATGAATTTTGATATCTTTATACTTGAATTTCAGATCATGATTAGCTTAACAAGAACCAAGGAAAAATGTATGAATATGTGAGTGTTGTTACAAGATGAAAAATGCTGCAGGTATCAACACTGTTGGTTACAACTGTGTCTTCTTTACTATGATAGGAGCATGTAATGTGGAATTCTTCTTAAATCTTGCATATCTTTATCTCATCAAACAAAGGGGTCCAAGTTCAGTTTTAAATAAGCATTTAAGGCAGATACTGACAACAATCTCATTTTTTAAAATGTTGTCTTGAGACAAATAATTTGAAATTTCTAAATTGGGAGTTTGAATCACTTTTGAAAGCTCTTACTTTCTTAAGCTGTCAGGTTTGTACCGACATGGAGTAAACAGCTATCATAAACGTAAATCTCCAAAACTAGTAGAAATTATGTCATGATTGATGGTTAAGATACCATGTCAGGGATTGTCTTTTCTTAGAAGTAGTGAAAGCTACTTACTATGACAATCAGACCTTCCTTGTATGTCAAAATGCTGGTGTGGAAGGTGGTGGAGCCCGTGCTGCTCTGTCTTAACTATGAGTGTGAGCTTTAAAGCTCGTTGATGAGTGGTAGCCAGCAAAGCCTAGAGCAACAAAAGCTTCTACAAAGGAACTAACCAAGAACAAAGAAGGGTTCCCAATTAAAGATCACATTCAGGGTTAAACTTCCAAAGGAGACATCCTGATCCTGGTTTTGTGCTGGCCTGGTACTCAGTAGGTTTTTGCTGTGAGGTTAAAGACTTGCCAGGCTGAACTTCGAAACAGTTTTTCTGTTGCACAGTATGATGTAACAGTCCATCTCTCAATGCAATAGGTATCAGTGGCCTCGTGAGCTTCTTCACAATATTGATATGTCTTCCAGCCCATTGAACCTGGACTGCAGAAGGCCCCATGTCATGTGTGAGCTCAGCCTGGATGCCAGCATTGCTGCTCCTCTTAGTTCCGTTTCTCGTGGTCACTTTACTACGAGAAACGCTGATTGGGTTTTCGTAGCTGTGTTCCAGGTTTTTAGTATCAGAACTATTCTTTCTTTAACCTCTATTCATATTTTCTCTACTTGAAGTTTTACATTCAGGAAAACCTCAGCTCAGGACTACTATGTACCTCCCCTTTGGAGGGAAAAATTATTTTAGGTAAAAGGCAAAAATTTTTTAAAAATATTTTTATTTATAATTATATGGAAGGGCCCTACCAAGATGCTAGAAATATAGGGAGTTCCTGACAAGAAATTTCCATTCTTATTCTGAAGAATTGCTTTCTTACTTAAAAACAAAGACAGTTTGTGAGTAGTTCTGGGCAATAGGGATAAATATAAAACAATAATGATGATCATTTTCTACATCTCATTATCAGCTGAGGTACTGTATATTACTGAATTTATTGAAGATAGTTATGTCTTTTAGACATTGTTGTTATAAACTATGTTTAAGCCTACTACAAGTGTTTCTTTTTGCATTATGTTGGAATTGATGTACCTTTTTTATGATTACCTCTCTGAACTATGGTGTGAACAATCAAACAAAATGATGAGATTAACGTTCATGGATAAATTCTAAGAAAACTAGTGTATTTTTTTGAAAAGTTTGAAGTTAGAACTTAGGCTGTTGGAATTTACGCATAAAGCAGACTGCATAGATCCAATATTGACTGACCCAAGCATGTTATAAAGACTGACATTTTAGACATTTTGAAGGCCCTGTAAGTGTTTATTAATTAGTTAGAACTTAATTGATTAAAAAATATATCCAAAGCACTATAGGCATTAGAATTCGTGCATCAAGAAATGATGACAAATAATACTGTTATTTATATAAATAACTAAAAAGGGTGTCTAATGAAGAAATATATTTTATTACAAAGAAATTATAAAACATTTTGAAGATTATATGCTTTAAAAGTTTAAGATGAAAAAATAATCAACCTTAGAAAAAATGTATAAAAATATATAAATTGTTAATGTCATTGATTAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000032487-Ptgs2:NM_011198:9
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
Alternative protein isoforms





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.000 A=NA C2=0.088
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0309810=An_peroxidase=FE(13.4=100)

							
A:
NA

							
C2:
PF0309810=An_peroxidase=PD(27.1=72.3)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000035065





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
NA
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr1:186674763-186675248 
ALTERNATIVE
HsaINT0134078
(PTGS2)
Human
(hg19)
chr1:186643895-186644380 
ALTERNATIVE
HsaINT0134078
(PTGS2)
Rat
(rn6)
chr13:67356255-67356510 
LOW PSI
RnoINT0119755
(Ptgs2)
Cow
(bosTau6)
chr16:69265750-69265898 
ALTERNATIVE
BtaINT0110440
(PGHS-2)
Chicken
(galGal4)
chr8:9815989-9816143 
ALTERNATIVE
GgaINT0039207
(heme)
Chicken
(galGal3)
chr8:10064692-10064846 
LOW PSI
GgaINT0039207
(PGH2_CHICK)
Zebrafish
(danRer10)
chr2:21259109-21261108 
LOW PSI
DreINT0121676
(ptgs2a)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
CAAAGGCCTCCATTGACCAGA

				
R: 
GCTCGGCTTCCAGTATTGAGG

				
Band lengths: 
302-585

			

		

	





	
Functional annotations
(Submit an annotation)

	


There are 0 annotated functions for this event 


		










GENOMIC CONTEXT[edit]












INCLUSION PATTERN[edit]






SPECIAL DATASETS
  • Pre-implantation embryo development
  • Muscular differentiation time course
  • Spermatogenesis cell types
  • Reprogramming of fibroblasts to iPSCs
  • Hematopoietic precursors and cell types






Retrieved from "https://vastdb.crg.eu/wiki/Special:VastDB"